[R] .Rprofile interfering with update.packages()

[stephen sefick]

I know this is a double post, but the subject line was really
misleading.  Sorry again.

This is the first time that I have tried to update packages with a
tinkered around with .Rprofile.  I start R with R --vanilla and it
does not load my .Rprofile, but when I issue the command
update.packages() R downloads the packages as expected, but then seems
to load .Rprofile before compiling the packages sources.  What am I
doing wrong?
kindest regards,

Stephen Sefick

see- Session info output and .Rprofile

Ubuntu 10.04
R 2.11.1

Session info:

R version 2.11.1 (2010-05-31)
x86_64-pc-linux-gnu


locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=en_US.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] graphics  grDevices utils     datasets  stats     grid      methods
[8] base

other attached packages:
 [1] gpclib_1.5-1            StreamMetabolism_0.03-3 maptools_0.7-34
 [4] lattice_0.18-8          sp_0.9-64               foreign_0.8-40
 [7] chron_2.3-35            zoo_1.6-3               vegan_1.17-3
[10] ggplot2_0.8.8           proto_0.3-8             reshape_0.8.3
[13] plyr_0.1.9


.Rprofile:
#source USGS graphing function for base data
source("~/R_scripts/USGS.R")
source("~/R_scripts/publication_ggplot2_theme.R")
source("~/R_scripts/llScript.R")


#set help_type
options(help_type="html")

#exit to get around anoying q behavior
exit <- function(save="no"){q(save=save)}

#most used libraries
library(ggplot2)
library(vegan)
library(StreamMetabolism)

#allow gpclib package to be used
gpclibPermit()

-- 
Stephen Sefick
____________________________________
| Auburn University                                   |
| Department of Biological Sciences           |
| 331 Funchess Hall                                  |
| Auburn, Alabama                                   |
| 36849                                                    |
|___________________________________|
| sas0025 at auburn.edu                             |
| http://www.auburn.edu/~sas0025             |
|___________________________________|

Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods.  We are mammals, and have not exhausted the
annoying little problems of being mammals.

                                -K. Mullis